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Midterm 2 Notes:

Species - A group of populations in which the individuals are so
closely related in structure, biochemistry, and behaviour that they can
successfully interbreed.
When and how do we get new species?
It is estimated that there are 8.7 million species on the planet today
** If you take the Linnaeus classification, you can run a mathematical
algorithm to examine the ratios when they did this, they found a
constant algorithm amongst all the organisms this algorithm is how
we got our 8.7 million species however, we have only identified 1.11.3 million
** Its going to take a VERY long time (1200 years) to identify all the
rest of the organisms but we are losing diversity faster than we are
able to characterize it
BIOLOGICAL SPECIES CONCEPT: species are groups or potentially
interbreeding populations, which are reproductively isolated (reproduce
sexually) from other groups species have their genus and species
name, which is their internationally recognized name (it is a unifying

Canola can be a problem for the name the person who named the
rapeseed plant, they gave the presence of this toxic element so the
world identified it as something toxic even though we had bread it out
of this toxicity a new named was requested and canola oil became
third most consumed oil by humans
Cant prove reproductive isolation to fossils, cant apply it to fossils

PHYLOGENETIC SPECIES: If you made a branching diagram of all

organisms, and there are organisms at the tip of the tree, then these
organisms can be identified as phylogenetic species well a cladogram
never stops branching but at that point you can resolve to fossils to
define similarities
ECOLOGICAL SPECIES: Not viable concept- grouping organisms that are
grouped as a result of the environment cannot be said to be related
look in a pond with algae, fish and turtles, they all cant be said to be
MORPHOSPECIES: Most prevalent concept today; morphological traits
that are used the distinguish between organisms.

Subspecies: a taxonomic group that is a subdivision of a species:

usually occurs because of isolation within a species (dog comes from
work example)
* They are organisms that are on their way to some sort of isolation
from each other

There is an isolating mechanisms in place that can drive the organisms

to become separate species, but they can still come back and
interbreed with each other
Examples are the snakes moving around in the states in the cross
over areas they can interbreed but in the distinct areas, they become
reproductively isolated
Example: the salamanders that move around the dry zone in California
and become reproductively isolated and are then able to interbreed on
the other side but this mating (the hybrid) is no extremely viable and
able to protect itself- disruptive selection

Ring species

A species with a geographic distribution that forms a ring

around an uninhabitable terrain.
Gene flow between distant population occurs only through
intermediary populations
Example: Salamanders of California, rattle snake
Still capable of interbreeding on border between zones
(transition zone)
These become different sub species, each zone is a different
sub species, but the all under the same species


Species formation
3 types:
Allopatric (isolation)
Parapatric (barrier spanning)
Sympatric (contiguous/touching populations)
Ex. Rape seed oiltoxic seed removed creating the
subspecies, Canola Oil.


Taxonomic subdivision of species

Local variants of a species

Reproductive Isolation

Ecological Isolation: frog is aquatic, another one is not as a

consequence, the two are in completely two different habitats and
never come into contact
Temporal Isolation: one animal will go into reproductive cycle at
different times of the year, no potential for cross breeding
Behavior: like hearing songs from one another or the flash signals
from fireflies textbook example is firefly and only come towards
each other when correct species signals the bilingual fireflies draw in

the wrong ones sometime one will devour the other when this
Mechanical: like a lock in key, only some species can fit together and
Gametic: eggs will not be fertilized by any sperm must be the sperm
of the same species there are recognizers on outer membrane of egg
to detect it


Hybrid inviability zygote never undergoes development/maturation

Hybrid sterility product of the two cannot produce any offspring and
will be sterile (like donkey and horse producing the mule)
Hybrid breakdown the hybrid is not as viable as the species that were
involved in the cross

Allopatric Speciation Vicariance

When environments separate, two populations are totally separate,
and they separate completely and will never come back and breed
even if the barrier is broken down
When the continents separated, species/ groups were separated
In Africa, the mammals remained and in South America kept the
At one point they touched, and mammals killed all the birds
Allopatric Speciation Dispersal

The founder effect: if the separation occurs and it goes to the extreme
and allows for new species to occur
Organisms get dispersed to new habitats and create new species

Grylloblattid Ice Age Vicariance

It is a survivor of the last ice age, lived on tips of ice on sheet on

Became so adapted to cold temperature, if the body temp raises, we
kill it
It is functional at negative 10/15 degrees, eats immobilized animals
Became isolated on the tops of these mountains, still there todays
Gave biologists mapping of first refuge areas during ice age
Important because this is how we know humans tapped into refugee
areas during the ice age and migrated towards North America

Sympatric Speciation

No geographical separation separating happens within one

Over time the seeds were driving the disruptive selection of the
insects depending on which seeds they will pierce


Meiosis fails, and something has diploid instead of haploid, results in

doubling of chromosome number
The hybrid will thus be genetically isolated
Or alloploid: two different species combine to create new
chromosomal compliment
o Example: Wheat is a pollyploid from three different species that

Classification: Categorize & group (ex. Sort stamps based on

country background)
o Dichotomy: Yes/No responses present in all organisms
classified (plant opens stoma?)
Present in all hierarchies/branches in phylogenetic
- Taxonomy: Using a set of rules to group organisms
o Folk: Medicine men, shaman (1 person in ancient cultures)
classified organisms; these guys can memorize (verbal);
tier of 2 or 3 hierarchies; 500 organisms; dichotomy of
plants and animals; dichotomy of medicinal plants; Eskimo
& Tropical people different types of animals present
o Artificial: Aristotle (animals) & Theophrastus (plants)
travel world; 1000s organisms recorded in writing; hence
considered fathers of taxonomy
o Mechanical: Linneaus (botanist but think as librarian);
organizes these big lists; creates kingdom of plants and
animals (dichotomy); huge phylum vermes(worms; long
cylindrical without legs)
o Natural: Darwin; evolutionary; using morphology; physical
appearance(no genetics atm)
Homoplasy (analogies) to Homology (share common
descent that indicate these organisms are grouped
together & distinguish from Convergences)
Homology: bats wings, flippers, legs, but still
similar bone structures (ie.Related
Ex. Jaw reinforcing structure; bone becomes
vibrational transmitter to perceive sound
(evolution of vertebrates)
Convergences: environmental drivers to develop
structure with similar function
Homoplasy: Separate organisms using flight since no connection
(insect wing, bird wing) Dont want to classify organisms as same only
because all have flight ; Analogous
What came first? Advanced (derived) VS primitive ;
very subjective since different characters was
weighted different
Subjectivity ex. Walcott (big scientist) says
Burgess Shales; he says shales derived from
arthropods (no further variation); two
graduates 15 yrs ago looks at them again &

discovered shales depicted Cambrian

Explosion(huge variation in organisms)
Types of Characters to separate organisms:
Morphology, Ultra-structure, Embryology,
Behaviour, Fossils, Molecules
o Phenetic (Numeric) Taxonomy:
Phenotypic measurements (empirical);
statistical method (Cluster analysis) to
determine evolutionary paths; rid of
subjectivity; based on statistical correlation
(genetic factors); Killed subjectivity atm!
Douglas Adams (3rd age of sand): as
computation increased, evolutionary paths
change; back to square one; use my program,
its better than your program (subjectivity
o Phylogenetic Taxonomy: Henning (entomologist);
cladistics to make evolutionary trees; provides us with
cladograms (rid of subjectivity completely)
Types of Phylogenetic Trees
Dendograms (top of tree = ideal form =
human race on top; similar to scala naturae)
Cladograms; sister group (ancestor); One
change results in separation of all other
organisms from sister group;
Clade: A subset of organisms within a group
that have all the same shared characters are
referred to as this and give this method of
classification its name (CLADISTICS)
o Node separates organisms based on
change of another characteristics;
o Polytomies: Polytomy is a term for
an internal node of a cladogram that
has more than two immediate
No resolution on what kind of change but there is a change

o Could be genetic in N-bases; shared

derived change
o Useful characteristics:
Apomorphies: Derived characters
(bird) (triploblastic)
Plesiomorphies: Primitive
characters (lamprey) (diplo..)
Synapomorphies: Shared
derived traits between organisms
(changes in evolution; we care
about this
Symplesiomorphies: shared
primitive(ancestral) traits between
o Anatomy of cladogram:
Monophyletic: Systematists excited
about monophyletic synapomorphies
Shared characters between
Polyphyletic: Convergence; but has
wings ex.
Paraphyletic: Bird different than Reptiles
- Creating a Cladogram:
o Different organisms with different characters being
o Create matrix with sister group zero for all characters since
completely plesiomorphic

o Different wars to arrange cladogram; there are chances for
all of them but evolutionary and statistically speaking,
there would be an inclination to choose the one that has
less changes; Parsimony.

Systematics: Application of evolutionary theory: Based on

common ancestry for classification system
Hierarchical: Linneaus, D,K,P,C,O,F,G,S; classification schemes
& systematics are present in hierarchies (ie. In Kingdom, In

Tend to classify organisms in a dichotomous manner (Yes or

No) for simplicity
When morphological data are combined with molecular data, we can
see advances in our understanding of evolution
and Adaptive radiation.
Ex. Bats & their habitats rediscovered via a combination of these two.
Hadean eon and Archean eon:
Geological Time Scale (Major Eons): Hadean and Archean (this
Hadean (4,600 3,800 Ma)

Formation of solar system and planet, ends off with origin of life

Archaean (3,800 2,500 Ma)


Anaerobic bacterial life, oxygen starts to accumulate in atmosphere

(Archea live in extreme conditions)

Proterozoic (2,500 543 Ma)


Oxygen atmosphere, single celled aerobic organisms

Phanerozoic (543 Ma to Present)


Multicellular organisms

Hadean Eon:
Building Phase:

Meteorites that contained lots of minerals (C, H, O) crashed into Earths

surface and provided it with the basic building blocks of life.
At this point, Earth is still a molten ball and meteorites are still flying
into it on a regular basis

Stabalizing Phase:

Earth starts to develop a crust on top of the molten lava

Earth is unique in which its mass is able to hold in an atmosphere so it
could trap in the molecules needed to survive
The water vapour in the air starts to cool down and water starts to
accumulate on the Earths surface which formed the oceans.
However, if another meteorite strikes then the water is Vapourized
(Evaporation) because of the intense amount of heat created by the
impact and the cycle starts over again.
Meteorites stopped hitting the Earth at the end of Hadean Eon


Life came from extraterrestrial origins.

No conclusive arguments (bacteria came from meteorites to Earth)
We still dont know WHERE exactly life came from
Hypothesis that proposes life on Earth was transferred from elsewhere in the Universe


All life on earth is carbon based. (Silicon has the same properties as
carbon and somewhere in the universe there might be a whole parallel
forms of life all based on silicon instead of carbon Silicon used in
computer chips here on Earth)
Carbon is the ideal lego block for building larger structures
(organisms). This is because carbon is a perfectly symmetrical element
(tetrahedral orientation of its electrons).


Water sticks to other objects

The adherence of molecules to the walls of conducting tubes, as in
Explains the meniscus you see in test tubes, etc.


The high resistance of water molecules to separation.

Water has a high tendancy to stick together due to polar
Surface tension is an example of cohesion

Surface Tension:

The force that places water molecules under tension, making them
harder to separate than the water molecules under them. At the top,
water molecules are in contact with air, so surface tension is created.
Some insects are able to walk on water due to surface tension. (Due to
o Reduce the surface tension of water by absorbing at the liquidgas interface

Can also form micelles and vesicles in water. When micelles

form, polar phosphate heads stick out towards water, and tails
form a core that can encapsulate an oil droplet.

Non-Polar Compound:

The dipoles of the element cancel each other out

Symmetrical distribution of charge, so that no positive or negative
poles exist ex. Hydrocarbons
Non Polar Covalent bonds:
o Have equal sharing of the bonding electron pair (one element
does not have the electrons more than the other)

Polar Compound:

Water is an example of a polar compound

An uneven distribution of charge, one side of the molecule is more
negative or positive than the other side
Ex. H2O The oxygen is more negative in charge than the hydrogens,
net dipole is not zero,
Polar Covalent bonds:
o Unequal sharing of electrons when bonding in this manner.
Reason is difference in electronegativity.

Hydrogen Bond:

Is the attractive interaction of a hydrogen atom between an

electronegative atom such as fluorine, oxygen,
Hydrogen bonds are INTEROLECULER! Between molecules, not
between atoms.
Occurs in water (inorganic) and DNA (organic)

Crystal Lattice of Water:


Is a very exact organization of water molecules to form a crystal like

When water is cooled down, it gets denser. When it reaches 4C
exactly, water forms a crystal lattice, which gets less dense because
the atoms are more spread out.
The lattice insults and maintains the temperature of the water under it,
allowing organisms to survive in the liquid portion.

Interstellar Space Dust:


The solar system was formed by the gravitational condensation of

Space Dust (consisted mostly of H)
Condensation of interstellar gas forms stars, and its consequence is
formation of planets (such as earth)
There are probably many millions of planets in our galaxy (because so
many stars)



Is a large molecule that bonds to other monomers to form polymers

Ex. Most common monomer is glucose (forms cellulose, starch, chitin,


Are polymers produced by living organisms
Ex. Cellulose, starch, proteins, peptides, DNA, RNA, lipids
Monomeric unites are: sugars, amino acids, nucleotide, glycerol & 3
fatty acids (respectively)

Chemical Evolution
Biological Evolution







Chemical Evolution: *refer to flow chart*


The abiotic (non-living) synthesis of organic molecules such as amino

The assembly of complex organic molecules from simple molecules,
including protein, RNA, or both
The aggregation of complex organic molecules inside membranebound protocells
Prebiotic soup, hydrothermal vents, interstellar organics, miller-Urey,
Biopolymers, Biomonomers
RELATE TO protocells, prebiotic soup, hydrothermal vents, etc.

Interstellar Organic Compounds:


Organic compounds coming from meteorites (C, H, O, N, etc.)

However, the heat may have destroyed these compounds upon arrival
on Earth

Miller Urey Experiment: (Proof)


Oparin and Haldane suggested that ultraviolet light (from Sun because
no O3 layer at the time) and lots of lightning provided enough energy,
with combination of a reducing atmosphere, to spark the
accumulation of simple building blocks of life.


Components of a reducing atmosphere: hydrogen, methane, ammonia,

water vapour
After recreating the atmosphere of the late Hadean Era, they found
acetate backbone, amino acid backbone, as well as other basic
building blocks
Prebiotic Soup: Reigning theory proved by Miller Urey experiment
o Life sprang from non-life (various chemicals in early Earths
o Spontaneous generation/origins had occurred (making of the
first nucleic acid) because of the lack of oxygen in the air,
however, it is unable to now (O2 in atmosphere) because the
conditions found in early Earth have changed
o Suggested that amino acids were chemically combined and
cooked by various sources of energy (lightning, ultraviolet
rays, etc.)

Green House Gases:


Carbon dioxide, Ammonia, etc would massively build up in the early

stages of Earths formation (end of Hadean Eon)
These gases helped to create life on the planet (prebiotic soup,
hydrothermal vents)
Currently these gases are bad for our society. It is kind of ironic that
these gases are what started life on Earth, however, these gases are
the very same that will most likely end life on Earth as well (global

Reducing atmosphere: (Related to early earth and how it was able to

create electron-rich molecules)

Refers to large amount of H2, Ch4, NH3 available on primitive earth

(fully reduced)
All the molecules were fully reduced, so electrons where able to be
shared very easily
Counter Abundance of O2 prevents complex, electron-rich molecules
from being formed
(Oxidizing Atmosphere)

Hydrothermal Vents:

Are highly reducing conditions. These vents were found on the ocean
These vents release geothermally heated water, methane and
ammonia, which may have lead to the basic building blocks of life on
primitive Earth
Organisms that thrive in this environment are of great interest to
scientists because of their ability to survive in such extreme conditions

Protocell/Protobiont: (Biological Evolution)

A group of abiotically produced organic molecules that are

surrounded by a membrane or membrane like structure.
Allowed a closed space for the molecules to order and organize
themselves because it was distinctly different from the outside
environment. (higher/lower concentrations inside or outside of
Protocells are said to have formed spontaneously due to the conditions
of primitive Earth- (relate to prebiotic soup) Spontaneous Origins
(protocells produced abiotically, panspermia, etc. Relate shittt)
They carry out metabolic reactions (Glucose-phosphate -> goes
in....Glucose + phosphate come out separate)

Central Dogma:

Flow of information from DNA to RNA to Protein.

Replication, transcription, translation
There is no way we can artificially make nucleotides, there we cannot
synthesize proteins on our own
Link to RNA WORLD!!

RNA World:

In CONTRAST to Central Dogma, early life on earth may have existed in

an `RNA World`
In primitive earth, suggested that RNA was the carrier of both
information as well as its own catalyst.
Nowadays, we have DNA and protein catalysts that do this for us, and
RNA is just the messenger between the two.
This is because DNA (information storage) and catalysis (protein) do a
far better job than just the RNA by itself. (evolution)

Proteins First Hypothesis:


Suggested that a small population of RNA molecules evolved and could

catalyze the formation of very simple protein, independent of the
This is a major leap for protein synthesis because proteins are far more
versatile than RNA molecules.
2 Reasons why:
o The catalytic power of most enzymes is much greater than the
o Proteins are much more diverse than ribozymes. 20 different
types of amino acids can be incorporated within a protein
whereas the ribozyme only has 4 nucleotide bases.


Hypothesis that solid surfaces (clay) would have provided a unique

environment for polymerization to occur.


Like water (or any solvent). Ex: phosphate head (lipid bilayer or


Does not like water (or any solvent) ex. Fatty acid tails (lipid bilayer or


Hydrophobic fatty acid tails face the inside of the sphere so

does not get `wet`
Hydrophilic phosphate heads face towards the surrounding
solvent (water)
o Lipid cells will divide and grow on their own. Protein
and nucleotides are being made in microspheres

Emergence: What is life and emergence?


More than the sum of the parts

Organicists (1930): vital force replaced by genetic program and the
importance of emergence.
For amino acids: they are more than just that
o Haemoglobin is the binding protein, as soon as one oxygen
binds, next three bind immediately

What is Life?

Self Replicating: life from life with genetic program

Metabolizing: Capturing and releasing energy
Self regulating: A delicate balance (homeostasis)
Reproduce: life from life (cell theory)
Evolving: adapting and changing
Responding: Sensing and interacting with surround world
Growth: increase in size (cell theory)

Archean Eon
Archea: none are pathogenic

One of 2 domains of prokaryotes

Share some traits that of bacteria and prokaryotes, however have
some unique characteristics as well that sets them apart into their own
They strive in harsh climates and extreme conditions (hydrothermal
vents, volcanoes, Primitive earth, etc.)
o Late hadean eon was the ideal time for Archaea to flourish
because there were such extreme conditions
o The reason for their success among harsh climates is that they
have differences in their plasma membrane (polar heads on both
sides, isoprene tails rather than fatty acids) which make them
more resistant to disruption (better for extreme climates)

Bacteria (Eubacteria):

bacteria have been present for a long time

bacteria haven't changed from their fossilized ancestors
considered "living fossils"; doing the same thing as they did 2 billion
years ago


Organisms that need oxygen to survive

Final electron acceptor is Oxygen (called aerobes can be obligate or
obligate anaerobes)
These organisms accept ONLY O2 as the final electron acceptor in ETS
(ex. Humans)


Organisms that DO NOT need oxygen to survive

Final electron acceptor may be metals (ex. nitrate or sulphate)
These organisms accept metals as final electron acceptors in the ETS
(anaerobic respiration)


Organism that produces its own food using CO 2 and sunlight (as well as
other small inorganic molecules)
o Plants are autotrophs, produce their own food, some bacteria
may be autotrophs as well
o Conversion of light energy (sun) into chemical energy, sugar,
and organic molecules. (Inorganice to Organic)
o Autotrophs use photosynthesis to get their energy and food


Area of the cell that contains the tightly packed chromosome

(condensed DNA molecule)
The chromosome is not contained in a membrane.


Small circles of DNA

Contains genes for non essential, however, beneficial functions (ie.
Antibiotic resistance)
Replicate independently of the cells chromosomes and can be
transferred from one cell to another
Through the process of conjugation
This way bacteria can spread their Antibiotic Resistance to other
bacteria very quickly in a population


Primary component of bacterial cell walls

It is a polymer of sugars and amino acids (forms linear chains)
(sort of like the ribose (sugar) attached to the nucleotide bases in DNA

Peptide Cross linkages between chains give the cell wall great
strength and rigidity

Gram Positive/Negative:

Bacteria can be divided into two broad groups depending on their

reaction to the Gram stain procedure:
o Gram Positive bacteria:
Cell walls composed entirely of a single thick
peptidoglycan layer
The stain sticks better
o Gram Negative bacteria:
Has two layers, thin peptidoglycan layer just outside the
plasma membrane, and an outer membrane
This type of bacteria defends from foreign invaders better
Almost all pathogens/diseases are Gram Negative
Is a germ that causes infection or disease or illness
to its host.
All pathogens are Gram negative bacteria

Cyanobacteria: Gram-negative photoautotrophs bacteria


Were so abundant that almost all O2 released was from them lead to
evolution of eukaryotic cells and aerobic respiration.
By product of Oxygen (first EVER photosynthesis water splitting
This sets the stage for aerobic metabolism and everything else that
was able to live
This is the most important group of bacteria

Morphological Diversity:

Bacteria described and named on morphology (Size, Shape, Mobility)

Bacteria Flagellum:

Made of single protein called flagellin.

Moves cell by rotating Flagellum
Prokaryote flagella protrude through the membrane - >

Bacterial Reproduction:

1. Binary fission
- Prokaryotes undergo a cycle of growth, DNA replication, and cell division,
producing two daughter cells from an original parent cell.
- This way of reproduction, there is no variation; Cells simply clone themselves
- Good for increasing numbers but not variation
- Scientists believe that Mitosis evolved from binary fission
2. Conjugation
- Plasmid transfer
- Process by which a copy of part of the DNA of a donor cell
(Plasmid) moves through the cytoplasmic bridge into the
recipient cell where genetic recombination can occur
- This process of reproduction provides immense amounts of
variation. (If one bacteria has the antibiotic resistant gene, then
it can share that with other bacteria through this process.
3. Transformation
- Bacteria can incorporate foreign DNA fragments into their own
- Bacteria are constantly swapping their DNA either by
conjugation or transformation
- This is the GREATEST source of variation
- Example: If bacteria didnt have the ability to digest lipids,
however picks up some DNA coding that allowed for digestion of
lipids, then it would have that ability.
4. Transduction
- Occurs when a virus (phage) infects a bacterial cell

The bacterial cell breaks down its DNA and incorporates it with
the viral DNA so it will be in the capsids of the virus.
Once Enough phages have replicated themselves in the cell, the
cell then bursts and viruses are released ready to infect other
o However some of the viruses that were in the released
cell now contain the bacterial DNA instead of the viral
DNA, or both

ATP Synthase:

Is a protein complex that is all over the membrane

It couples the transport of proteins across a membrane to the synthesis
of ATP
The spinning of the headpiece in ATP Synthase represents the smallest
molecular rotary motor known in nature (ATP universal high energy

Cellular Respiration:

NAD+ -- receives electron; becomes high energy; reduced to NADH

need to take high energy electron and turn back to original state; try to
trap as ATP;
mitochondria -- electron being passed between series of processes ion
the ETS
o all eukaryotes are restricted to energy from sugar
o prokaryotes (bacteria) can use just about anything to obtain its
Electron Transport Chain (ETS): series of oxidation and
reduction reactions
o The NADH synthesized by both glycolysis and the citric acid cycle is oxidized,
with the liberated electrons being passed along an electron transport chain until
they are transferred to O2, producing water. The free energy released during
electron transport is used to establish a proton gradient across a membrane, and
this, in turn, is what synthesizes the remaining ATP.

Electron Donor:

Donates electrons to other compounds

o Leaves itself being oxidized, while the compound it donated its
electron to is reduced.
o Some early cells developed the capacity to carry out photosynthesis using water
as an electron donor ; the oxygen produced as a by-product accumulated, and
the oxidizing character of Earth's atmosphere increased


Compounds that are oxidized get stripped of their electrons (while reducing other
compounds; adding electrons to other compounds)

Electron Acceptor:

Accepts electrons from other compounds

o Gets reduced by another compound. That other compound gets oxidized
(Stripped of its electrons)
o O2 is the final electron acceptor in the Electron Transport System (ETS)


Compounds that are reduced, accept or gain electrons from other

compounds. In the process, they oxidize, or remove the electrons from
the other compounds.


Process where electron carried by NADH are taken to an organic

acceptor instead of the ETS
o Lactic Acid Fermentation or Alcohol fermentation


Phototroph: use sunlight for energy, and CO2 as their carbon source
(Green plants)
Chemoorganotrophs: use organic compounds are their energy and
carbon source (glucose, acetate, etc.)
Chemolithotrophs: thrive in habitats such as deep sea hydrothermal
vents, where reduced inorganic compounds are abundant
o Their ability to harness energy from these compounds makes
them the foundation of the vent community (analogy plants
are like that for terrestrial organisms, rely on them to turn
inorganic to organic)


Photoheterotrophs: use sun light for energy, but cannot use carbon
dioxide as their sole carbon source
o They use compounds such as carbohydrates, fatty acids and alcohols as their organic

Chemoorganoheteroptrophs: requires organic substrates to get its

carbon for growth and development
o Example: Decomposers
Chemolithotrophic Heterotrophs:



An organism that gets its nutrients and energy from by eating other
organisms or their remains
o Animals, humans, etc.


Archea isolated to extreme environments


Hot springs, hydrothermal vents at bottom of ocean, and salt

extreme lovers


Type of layered rock that is formed when microorganisms bind particles

of sediments together, forming thin sheets

Nitrogen Fixation: Earths atmosphere contains approx. 80%

nitrogen gas (however has strong triple bond)

The strong triple bond that forms nitrogen gas is hard to break loose,
therefore is useless unless Fixed
Nitrogen fixing bacteria are the only bacteria that are able to take
inorganic nitrogen and convert it to organi
N2 is reduced to ammonia (NH3) and then quickly ionized to NH4+ to
make nucleic and amino acids
Is the only means of replenishing the nitrogen sources (Nitrogen cycle)
o Therefore all organism rely on nitrogen fixed bacteria
o Cyanobacteria is an example of nitrogen fixing bacteria

Bacterial Importance:

o How we first got into researching bacteria, by trying to figure out
the diseases it causes
Nitrogen Fixing
o converts inorganic N2 into organic nitrogen (amino and nucleic
acids) nitrogen cylce
o decomposes matter
Unique biochemical pathways
o Cyanobacteria (Produced most of the O2 in atmosphere to
sustain aerobic metabolisms
Extremophiles (Archea)
o Archea that have been around since end of hadean eon. Lived in
extreme conditions, hydrothermal vents, volcanic regions, salt
lakes, etc.

*Bacteria reproduce asexually*

*Bacteria are living fossils*
- couldnt have come before prokaryotic cells, because they need them to replicate
Virus Morphology
- Helical
- Polyhedral
- enveloped
- complex enveloped
Slide 38

All enveloped viruses have a phospholipid bilayer, plasma membrane which surround
the plasmid which surround the DNA (genome)
- non enveloped dont have the phospholipid bilayer
- alphanumeric way to distinguished between viruses
o H1N1 fingerprint profiling for viruses
Slide 39
Virus morphology
- Head contains viral DNA inside and capsid protein
- Tail - contains sheath and baseplate, recognition fibers
Slide 40
Viruses arent cells?
- no cell membrane
- no ribosomes
- no mitochondria
- DNA (RNA) wrapped in a protein coat
Side 41
Viral phases in replication
- Entry
- Transcription and viral protein production
- Replication of viral genome
- Assembly of virions
- Exit
- Transmission to new host
Slide 43
Viruses replication
- Lytic cycle
lytic cycle results in the destruction of the infected cell and its membrane
- Lysogenic cycle
Lysogeny is characterized by integration of the bacteriophage nucleic acid into the
host bacterium's genome or formation of a circular replicon in the bacterium's
Slide 44
Exit host budding
- or exocytosis
- breaks through the cytoplasm of host, then gains an envelop
Slide 46
Prions and Viroid
- bovine spongiform encephalopathy
- alpha and beta pleated sheets
- normal becomes aberrant
- mad cow disease
- Viroid; made up of circular RNA that is only a few hundred bases. Viroids infect
plants and cause irregular or stunted growth
- Viroids do not produce proteins and use host enzymes to replicate.
- Plant pathogens, of the order Viroidales, that consists of just a short section of RNA
but without the protein coat typical of viruses.
- Rna silencer, death of cell

- Hepatitis D a little RNA circle, travels with the Hep B virus,

- Prions;
Prions are infectious proteins that can cause many brain degenerative diseases
o Prions lay somewhat dormant in the brain for around a decade, which makes
uncovering the source of the prion virtually impossible.
o It is generally thought that a prion is a misfolded protein that somehow causes
neighboring proteins to misfold. So, once a prion is present, a chain reaction is set off
until almost all the proteins are prions, which will aggregate together.
- Still considered living because they do change over time, evolve, and reproduce

Proterozoic Eon
Eukaryote origins
An updated version of parts of this
document appear in Digital Diversity
as the topic Eukaryote
autapomorphies. Be sure to look this
Eukaryotes differ from their
prokaryote counterparts in a number
of ways, not the least of which is size.
Along with an increase is size is an
increase in cellular complexity
including an elaborate internal
membranes the endomembrane
system. Cells exchange materials with
their external environment bringing in nutrients and carbon dioxide if
they are plants, or oxygen of they are animals or fungi, across their
plasma membrane the interface with the external environment. They
also remove wastes across the same surface. Cellular function occurs
in the volume of the cell and the relationship between supply (surface)
and function (volume) is referred to the surface:volume ratio for the
cell. Very small cells have large surface areas and small volumes and
have no supply problems. Large cells dont have such an advantageous
ratio between the two and the exchange across the surface may not be
rapid enough to supply the volume of the cell. A solution to this
problem is to increase the surface area by folding the plasma
membrane inwards. There are examples of this in the larger bacteria

and it is the origins of the endomembrane system found in the

eukaryote cells.
Until the infolded membrane surrounds something to create a new
contained environment, which it doesnt in the bacteria, weve only got
folded membranes and an increase in the surface area. For the
eukaryotes the first material to be wrapped inside an endomembrane
system was the genetic material of the cell. The result is the nucleus
surrounded by its nuclear envelope and because it is formed from
invaginated membrane it has an inner and outer component and two
bilipid layers. Special openings, nuclear pores, in the envelope allow
RNA produced in the nucleus outside to the cytoplasm where it is
processed into final products which could include ribosomal RNA,
transfer RNA or proteins if it takes the form of messenger RNA. Unlike
the prokaryotes where transcription and translation both happened in
the cytosol (cytoplasm) the nuclear envelope separated transcription
inside the nucleus and translation outside. In eukaryotes this meant
that as mRNA was produced it wasnt immediately available for
translation because the translation machinery wasnt present inside
the eukaryote nucleus. Over time this probably explains why in
eukaryotes the original transcript from the DNA is often modified or
altered before its released from the nucleus. There is more to the
endomembrane system than just the nuclear envelope and it also
includes endoplasmic reticulum which can be either rough with
ribosomes or smooth if there are no ribosomes present. Other
components of the endomembrane system include the golgi complex,
vesicles and lysosomes.
The second major event on the evolution of eukaryote cells is the
origin of the cells power plant; the mitochondria. Our primitive
eukaryote cell was only capable of anaerobic metabolism to generate
ATP (fermentation) and consumed other small cells, notably bacteria,
as a food source. Normally they would destroy the bacterium but some
where along the line the bacterium survived and a symbosis developed
between it and the cell that surrounded it. As we saw in our discussion
on bacterial diversity, one type of bacterium includes
chemoorganoheterotrophs that use existing organic carbon molecules
as a source for the carbon molecule and, as it breaks the bonds to
release the carbon molecules, the bacterium captures the high energy
potential in ATP. This is exactly what mitochondria do; taking threecarbon pyruvate and turning it along with high energy electron carriers
like NADH into ATP and carbon dioxide. Because of the symbiotic
relationship the cell benefited from being able to shunt pyruvate to the
symbiont rather than using it for anaerobic respiration. The bacterium
provided ATP to its host and the host the three-carbon organic
molecule for it to use to produce ATP for itself and its host.
The end result of all of this is the eukaryote cell with a nucleus
separated from the cytoplasm by the nuclear envelope formed from

the endomembrane system, mitochondria and organelles that carry

out a variety of different specialized functions by the cell.
Evidence for endosymbiosis
As was just mentioned mitochondria arose as an endosymbiotic event
between a bacterium and a simple eukaryote cell with a nuclear
membrane and endomembrane
system. The question is, how do we
know that this is what happened?
There are a number of pieces of
evidence that lead us to this
conclusion. The first piece of
evidence is that mitochondria is
surrounded by a double bilipid
membrane. The inner membrane is
the original bacterial membrane. The
outer mitochondrial membrane was
produced by the cell as it surrounded
the bacterium in the membrane that
would have normally been a food
vacuole. The second piece of
evidence is that mitochondria have their own DNA which is circular, a
configuration that is typical of the bacterial genome. But its more than
just a circular configuration, the genetic sequence of the mitochondrial
DNA more closely resemble bacteria than the genome of the eukaryote
host cell. The mitochondria also contains it own transcription and
translation system using ribosomes that are bacterial in size, not the
size typical of eukaryotes. Perhaps the most obvious evidence is the
similarity between the size of mitochondria and bacterial and that both
use binary fission as a means of replication.
The chloroplast (plastid) also arose
by endosymbiosis, only in this case
an autotrophic phototroph
bacterium, most likely a
cyanobacterium, was internalized.
Again like the mitochondria theres
a double plasma membrane around
the plastid that also has its own
circular DNA resembling bacterial
DNA and bacterial type ribosomes.
Pearson Benjamin
In some algae the plastid still has
traces of the peptidoglycan cell
wall that is typical of bacteria.
So which came first, the mitochondria or the plastid? The evidence
suggests it was the mitochondria. Remember the prebiotic soup was
being used as a nutrient source for initial growth and there would be a
distinct advantage to have mitochondria. A photosynthetic

endosymbiont was certainly an advantage once it first appeared but

remember even a photosynthetic cell needs mitochondria to break
down carbohydrate to produce ATP. So while glucose is produced by
the plastid the usual metabolic process break it down into ATP and
carbons that can be used in metabolism and that requires a
mitochondria they came first.
There is a third example of endosymbiosis in the certain algal groups.
In this case a small eukaryote green algae is engulfed and surrounded
by a larger eukaryote and is set up in a symbiotic relationship. Because
the symbiont isnt a bacterium but anoth eukaryote this is referred to
as a secondary endosymbiotic event. One of the consequences of this
process, and piece of evidence for its occurrence is the membrane
structure of the chloroplast. In the initial algae it would have had a
double membrane but when its not host surrounds it there is another
membrane resulting in third bilipid membranes surrounding plastids
that have arisen from secondary endosymbiosis. There are two types
of algal plastids and each uses a different set of chlorophylls. In the
green algae both chlorophylls a and b are used in photosynthesis in the
red algae on chlorophyll a. Secondary endosymbiosis has occurred
twice with one algal group using the red algal plastids and the other
the plastids from green algae. If its not convincing enough that it has
happened at least twice there are living species that capture green
algae and uses them for short periods of time when they need to
obtain nutrients from photosynthesis when there
are non to be consumed allowing a heterotroph to
become an autotroph!

Viruses, prions and viroids

Viruses are also capable of replication and are
much smaller than bacteria and archeans. In their
simplest form, a virus consists of its genome
surrounded by a protective protein coat, the
capsid. The viral genetic information contains the
genes required to duplicate the viral genome,
manufacture the capsid proteins and assemble the
capsid around the copies of the genome. But,

Soldiers from
Fort Riley, Kansas
ill with Spanish
influenza at a
hospital ward at
Camp Funston in
1918, where the
North American
part of worldwide
US Army

viruses lack any of the synthetic machinery to carry this out. Instead
they take over the replication, transcription and translation machinery
of another cell.
Like bacteria, viruses are characterized by their morphology and have
one of two forms: non-enveloped or enveloped viruses. Both have the
capsid casing surrounding the genome but an enveloped virus has an
additional lipid bilayer membrane surrounding the capsid and the
genome inside. This lipid bilayer is formed from the plasma membrane
of the host and includes host membrane proteins and additional
plasma membrane proteins added by the virus.
We can use the influenza virus as an example of
how these additional viral proteins in the envelope
are used to identify the virus. There is a set of
proteins referred to as the H and N antigens
embedded in the envelope of the virus. The Hantigens are important in recognizing a host cell and
attaching the virus so that the genome can move
into the host cell. The N-antigens are involved in the
escape from the host cell when the virus has
completed replication. The influenza virus is given a
Structure of
designation with H and N numbers and in the winter
swine influenza
of 2010 the H1N1 variant was of great concern as a
virus showing
different type of potential pandemic virus. In 1918 the Spanish flu
antigens present virus killed more people returning home after the
on and inside the First World War than were killed in the war itself,
between 50 and 100 million people around the
world! The Spanish flu was also an H1N1 variant. For
M Eickmann,
non-enveloped viruses, the
proteins contained in the capsid
itself are used to identify the
different viral forms and the capsid proteins are
important in recognizing the host cell and assist
with the transfer of the viral genome into the host.
If we think back to the Archean eon, the oceans
were filled with bacterial life and there must have
been some checks and balances in place to control
bacterial numbers and this was probably one of the
original roles of viruses as, if you like, the predators
of the bacteria. They probably have a similar role
today. Viruses that invade bacteria are nonIn this
enveloped bacteriophages and they attach to the
surface of the bacterium and inject their genome
microscope you
(DNA or RNA in retroviruses). The result, protein
can see the
synthesis of host proteins is shut down and only
attached phage
viral nuclear material is duplicated and proteins for particles on the
the new capsid produced. The virus reassembles as surface of the
bacterial cell.
Graham Cohen,

new virions, a term used for a single virus particle, and the bacterial
cell breaks open, lysis, releasing hundreds, if not thousands of virions
ready to infect another cell. This sequence is the lytic cycle.
Sometimes the viral genome will incorporate itself into the bacterial
DNA and remain there, dormant. Each time the bacterium duplicates
the viral copy is duplicated and at later time the lytic cycle may
resume. This form of viral reproduction is the lysogenic cycle. When a
non-enveloped virus escapes from its host cell it kills the cell. Its a
little different with the enveloped viruses. In this case during the
replication cycles, the virus created the membrane proteins that are
added to the mix of proteins already in the hosts plasma membrane.
When the virus escapes it buds from the surface of the host cell and as
it buds it wraps itself in the host cell membrane.
So where do viruses fit into the scheme of things? For a number of
reasons viruses are not cells. They arent surrounded by the bilipid
layer that separates the inside of the cell from the outside. Although
there is a plasma membrane of sorts surrounding an enveloped virus it
does not have the dynamic functions of a typical cell membrane. The
synthetic machinery for protein synthesis is missing, as are the
mitochondria to fuel any metabolism. These last two raise the question
of whether viruses should even be considered living. Our criteria for
living include the following; the ability to replicate/grow, carry out
metabolism, regulate, evolve and respond to internal and external
stimuli. Viruses are only capable of one of these, evolving. They need
their host cell to be able to do the rest. You might
question whether they can evolve and its important
to realize the life cycle of a virus, lytic or lysogenic,
results in duplicated nuclear material that may be
different from the original - and that variation is the
basis of evolution.
Prions are small proteins that can exist in two
configurations: the normal, properly folded form and
a misfolded form. What is interesting about prions is
that if a misfolded version of the prion contacts a
normal one it converts the normal one into a
misfolded prion and now the two can convert other
prions. This results in explosive exponential growth
in the number of misfolded prions. Prion are
common on the surface of cell membranes and
shows the
vacuoles in grey although it is still not clear what their normal
function is they are believed to be involved in cell-to
matter of the
cell interactions; possible adhesion or
brain of a cow
communication. In other words having prions is a
with Mad Cow
Disease (Bovine normal thing. But when they are misfolded they can
form fibres and add more of the altered prions at the
USDA, Al Jenny,

tip, growing the fibre. The fibres often break and the number of
growing points increases and as the fibres enlarge they create
aggregates that appear as spongy holes in brain tissue. In animals this
is mad cow disease and in humans CreutzfeldtJakob disease. What
is particularly dangerous about the prion is as a small protein it is very
stable and hard to destroy. When animal by-products were used as a
protein feed supplement, prions passed from the
food into the brain tissue. But, remember prions
are not just in the brain they are in the membranes
of all the cells and if ingested as meat protein they
can survive the environment of the gut and infect
human cells! This is why mad cow disease is such a
danger in Britain 180,000 cattle were infected
and 4.4 million were slaughtered to eradicate the
disease. In Canada the disease appeared in Alberta
in 1993 and a second case in 2003 saw the disease
spread from Canada to the US and world embargos
on Canadian beef.
resulting from
Viroids are subviral particles consisting of a small
infection with the
piece of circular RNA that is capable of selfpotato spindle
replication. The genome is small compared to a
virus but you could consider a viroid to be a naked tuber viroid.
virus that has lost its capsid coat. When they were USDA, Barry
first discovered the ability for RNA to replicate RNA Fitzgerald
was the bases for the ribozymes and the proposal of an RNA world as
the origin of the replication, transcription and translation systems of
the Central Dogma of life. The RNA in viroid does not code for a protein
but single stranded RNA copies are capable of binding to the mRNA of
the host cell and when they do they silence the message which is not
translated into a protein. These are primarily plant pathogens but it
now appears the hepatitis D is an animal viroid that uses the hepatitis
B envelope to move from cell to cell.
Changing earth highlights
Proterozoic eon (2500 - 543 Ma)
2000 Ma - Oxidation produces "red beds"

1900 Ma - Oxygen levels reach 3%

1800 Ma - Oldest eukaryote fossils

1200 Ma - True algae

1100 Ma - Rodinia supercontinent forms

900 Ma - Soft-bodied animals

800 Ma - Major glaciation period begins

700 Ma - Breakup of Rodinia supercontinent

600 Ma - Protective ozone layer in place

543 Ma - Vendian extinction, Hard-shelled animals